40 Open source projects that are alternatives of or similar to adjclust

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

A faster lmm for GWAS. Supports GPU backend.

Genome Contact Map Explorer - gcMapExplorer. Visit:

Perform GWAS using the FarmCPU model.

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

dcHiC: Differential compartment analysis for Hi-C datasets

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Mixed models @lme4 + custom covariances + parameter constraints

Visual Machine Learning of Genome-Phenome Associations

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

Docker for 4DN Hi-C processing pipeline

Large genome reassembly based on Hi-C data, continuation of GRAAL

Quantitative Trait Cluster Association Test in R

A Python implementation of divisive and hierarchical clustering algorithms. The algorithms were tested on the Human Gene DNA Sequence dataset and dendrograms were plotted.

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

A 3D genome data processing tutorial for ISMB/ECCB 2017

Analysis of Chromosome Conformation Capture data (Hi-C)

machine learning algorithms in Swift

Rare variant test software for next generation sequencing data

📊 Identify cell types and pathways affected by genetic risk loci.

Find causal cell-types underlying complex trait genetics

GWAS summary statistics files QC tool

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

Python API for comprehensive GWAS analysis using GEMMA

Heritability, genetic correlation and functional enrichment estimation for case-control studies

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

Server component for HiGlass that manages and serves tiled data

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Builds a docker container wrapping higlass-server and higlass-client in nginx

Python code for common Machine Learning Algorithms

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

Clustering methods in Machine Learning includes both theory and python code of each algorithm. Algorithms include K Mean, K Mode, Hierarchical, DB Scan and Gaussian Mixture Model GMM. Interview questions on clustering are also added in the end.

A framework for building (and incrementally growing) graph-based data structures used in hierarchical or DAG-structured clustering and nearest neighbor search

Calculate similarity of sentences & Cluster the result.

Genie++ Fast and Robust Hierarchical Clustering with Noise Point Detection - for Python and R

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)